- HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it encodes information from identified or predicted protein interfaces in ambiguous interaction restraints (AIRs) to drive the docking process. HADDOCK can deal with a large class of modeling problems including protein-protein, protein-nucleic acids and protein-ligand complexes.
- More information about HADDOCK can be found on the HADDOCK website
- Reference for use of the server
-
S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin
"The HADDOCK web server for data-driven biomolecular docking."
Nature Protocols, 5, 883-897 (2010).
- HADDOCK webserver
- To use the HADDOCK docking server you must have registered for an account. If you do not have a account yet you can register here
- Note: The HADDOCK server might busy at times and/or closed to users because of workshops, tutorials or CAPRI runs. The Grid-enabled version of the HADDOCK server remains however always open. It does need a separate registration and a valid Grid certificate.
-
- HADDOCK server: the Expert interface (requires Expert level access)
- HADDOCK server: the Refinement interface (requires Expert level access)
- HADDOCK server: the Guru interface (requires Guru level access)
- HADDOCK server: the Multi-body interface (requires Guru level access)
The default HADDOCK settings used by the server can be found here
A list of modified amino acids supported by HADDOCK can be found here
- HADDOCK help center
- You can post question regarding the use of the HADDOCK web server using the WeNMR HADDOCK support center. To make use of this service you should first register with the WeNMR virtual research community (register link on the top right of the WeNMR page).
- Further the WeNMR site also provides a number of HADDOCK tutorials and a WIKI page to which you can contribute.
- HADDOCK webserver statistics
- Server statistics generated on: 2012-05-20 05:52:42
- Number of running requests: 11 , of which 2 on the eNMR grid
- Number of queued requests: 35
- Total number of served requests as of June 1st 2008:
27253
,
of which 3409 on the eNMR grid - Number of registered users: 2208 ( 1723 easy / 184 expert / 301 guru)
- Number of registered users for the grid-enabled portal: 131
- Server example
- An example of the server output for the e2a-hpr example provided with the HADDOCK distribution
can be found here. This is the result of a run
via the "easy interface" using only chemical shift perturbations as defined in the
HADDOCK tutorial.
- Tutorials
- A demo web form for the easy interface with pre-loaded parameters is available here
A demo web form for the guru interface with pre-loaded parameters is available here
A tutorial describing the use of the HADDOCK web portal with various combinations of data is available here
A tutorial movie is available here (requires Flash)
- Services
- Our software web portal is an easy gateway for you to use many of the powerful software packages developed in our group. Read a bit more about all the services that we offer and take a peek at the state of the art computer clusters that are running your calculations.
- Learn more >>
- Research
- Research within the computational structural biology group focuses on the development of reliable bioinformatic and computational approaches to predict, model and dissect biomolecular interactions at atomic level. For this, bioinformatic data, structural information and available biochemical or biophysical experimental data are combined to drive the modelling process. By following a holistic approach integrating various experimental information sources with computational structural biology methods we aim at obtaining a comprehensive description of the structural and dynamic landscape of complex biomolecular machines, adding the structural dimension to interaction networks and opening the route to systematic and genome-wide studies of biomolecular interactions.
- Learn more >>
- Acknowledgements
- The continuous development of HADDOCK and its web server is made possible thanks to the financial
support of several national and European grants.
- Learn more >>
- World map:
- Links:
- NMR Spectroscopy >>
The servers home, the NMR Spectroscopy Department - Bijvoet Center >>
The Bijvoet-Center for structural biology - Faculty of
Science >>
Faculty of Science main page - Utrecht University >>
Utrecht University main page